The Y chromosome holds great promise for human evolutionary research. Because of its paternal mode of inheritance and lack of recombination, the male-specific portion of the Y chromosome provides the best opportunity to test hypotheses based on maternally-inherited mitochondrial DNA. The overall goals of this proposal are to develop and use the Y chromosome as a tool to test hypotheses regarding 1) the phylogenetic relationships of humans and great apes, 2) the origin and migration patterns of modern human populations, 3) and male-mediated gene flow in selected regions of the world. This proposal delineates the first comprehensive effort to examine phylogenetically useful point mutations and insertion/deletions on the human Y chromosome. The distribution and frequency of a number of previously ascertained Y-specific polymorphisms will be determined in a sample of 2300 humans from all inhabited continents. PCR-based mutation detection methods such as single-stranded conformation polymorphism and DNA heteroduplex analysis, will be used to detect new Y-linked polymorphisms. Enzymatic mismatch cleavage, a new technique that offers several advantages over current mutation detection methods and promises to be useful for health-related research, will be developed. Rapid methods to genotype confirmed point mutations in large population samples will be devised. Furthermore, at least five kilobases of Y-specific single-copy DNA will be sequenced from 16 humans and four species of great apes (Pan troglodytes, Pan paniscus, Gorilla gorilla, and Pongo pygmaeus). These combined efforts will result in comparisons of approximately 24 kilobases of unique DNA per Y chromosome from humans with diverse geographical backgrounds. In addition to these comparisons of point mutations and insertion/deletions, the potential value of hypervariable microsatellite markers in assessing levels of genetic diversity, extent of gene flow and affinities among populations will be investigated. The data will be used to 1) construct Y chromosome haplotypes, 2) build phylogenetic trees of Y-haplotypes using great apes as an outgroup, 3) determine evolutionary rates of unique Y-linked sequences, 4) estimate the degree of genetic diversity in human populations and on different Y- haplotypes, and 5) determine genetic relationships among human populations. Current cladistic models will be explored t derive information about the age of Y-lineages, and the size and geographical locations of ancestral populations. This may help to distinguish whether contemporary Y chromosomes began diversifying before H. erectus populations spread out of Africa more than or equal to 1 million years ago, or more recently, during the rise of modern human populations. Finally, the data will be used to address hypotheses concerning male- mediated gene flow in Asia and Europe, and admixture in Japan. These paternally-derived data will complement the growing wealth of linguistic, morphological and archaeological data, as well as data derived from autosomal and mitochondrial DNA studies.